Related Experiment Video
Updated: Mar 15, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
Published on: May 31, 2011
RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes
Bruno Contreras-Moreira1,2, Jaime A Castro-Mondragon3, Claire Rioualen3
1Estación Experimental de Aula Dei-CSIC, Av. Montañana 1.005, 50059, Zaragoza, Spain. bcontreras@eead.csic.es.
Abstract:
The plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://plants.rsat.eu ) offers specialized options for researchers dealing with plant transcriptional regulation. The website contains whole-sequenced genomes from species regularly updated from Ensembl Plants and other sources (currently 40), and supports an array of tasks frequently required for the analysis of regulatory sequences, such as retrieving upstream sequences, motif discovery, motif comparison, and pattern matching. RSAT::Plants also integrates the footprintDB collection of DNA motifs. This protocol explains step-by-step how to discover DNA motifs in regulatory regions of clusters of co-expressed genes in plants. It also explains how to empirically control the significance of the result, and how to associate the discovered motifs with putative binding factors.
Related Concept Videos
Evolutionary Relationships through Genome Comparisons
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Microtubule Associated Motor Proteins
Cis-regulatory Sequences
Cis-regulatory Sequences
Cell Signaling in Plants

